[gmx-users] error in grompp command

Chandan Choudhury iitdckc at gmail.com
Thu Jul 3 12:34:48 CEST 2014 

Dear Rinu,
You need to arrange the gro file is the same sequence as in the top file
(or the vice-versa).

Chandan


On Thu, Jul 3, 2014 at 3:57 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello gromacs users now have been removed this error after changing the
> number of SOL in topol_popc.top file (counted from popc128.gro)
> after that i hav used -maxwarn 1 command
>
> result is
>
> Generated 813 of the 2346 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Warning: atom name 6657 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6658 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6659 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6660 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6661 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6662 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6663 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6664 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6665 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6666 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6667 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6668 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6669 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6670 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6671 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW
> - OW1)
> Warning: atom name 6673 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6674 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW
> - OW1)
> Warning: atom name 6676 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topolpopc.top, line 26]:
>   7380 non-matching atom names
>   atom names from topolpopc.top will be used
>   atom names from popc128.gro will be ignored
>
>
> Analysing residue names:
> There are:   128      Other residues
> There are:  2460      Water residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 34725.00
> Largest charge group radii for Van der Waals: 0.216, 0.216 nm
> Largest charge group radii for Coulomb:       0.216, 0.216 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115
> Estimate for the relative computational load of the PME mesh part: 0.36
> This run will generate roughly 164 Mb of data
>
> There was 1 warning
>
> how tom resolve these problems
> em.tpr is formed but rest of the files are not formed
> help
>
>
> On Thu, Jul 3, 2014 at 2:23 PM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
> > hello everyone
> > my grompp related   problem atomtype CA not found has been solved now i
> am
> > using 56a3 force field for protein ligand complex with popc but srill i
> > didnt get em.tpr a new error
> >
> >
> >
> > Excluding 3 bonded neighbours molecule type 'POPC'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.5
> > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> > 523
> >
> > Fatal error:
> > number of coordinates in coordinate file (popc128.gro, 14036)
> >              does not match topology (topolpopc.top, 17459)
> > kindly help
> >
> >
> >
> > On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
> >>
> >>> hello gromacs users
> >>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in
> the
> >>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both
> are
> >>> present according to tutorial i have been followed  all the step
> >>> still em.tpr not formed
> >>> atomtype CA not found
> >>>
> >>>
> >> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
> >> you're mixing and matching force fields (note that gmx.ff has been
> removed
> >> from the latest Gromacs version, since it should not be used).  Without
> >> explicit detail of your topology (i.e. post your files so they can be
> >> downloaded), there's very little that can be done to suggest where
> things
> >> have gone wrong.  I strongly suspect you've mixed and matched force
> fields
> >> somewhere, which is easy to do when dealing with complex systems.  Pick
> a
> >> force field, stick to it exactly.
> >>
> >> -Justin
> >>
> >>
> >>
> >>> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. <
> >>> valentina.erastova at durham.ac.uk
> >>>
> >>>> wrote:
> >>>>
> >>>
> >>>  Hi Rinu,
> >>>>
> >>>> See what forcefield files you include in your topology, then go to the
> >>>> force field folders and check if those indeed have that atom types.
> >>>> You must indeed be missing the CA type. Likely, you just forgot to
> >>>> include
> >>>> some topology file.
> >>>>
> >>>> V
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request@
> >>>> maillist.sys.kth.se
> >>>> <mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> >>>>
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> Message: 2
> >>>> Date: Wed, 2 Jul 2014 12:26:07 +0530
> >>>> From: RINU KHATTRI <nickname.mittu at gmail.com<mailto:
> >>>> nickname.mittu at gmail.com>>
> >>>> To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
> >>>> Subject: [gmx-users] error in grompp command
> >>>> Message-ID:
> >>>> <CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A at mail.gmail.com
> >>>> <mailto:CAOEfx3KBphAK_BRP4L4orCp_gSBsuSOHNLUgHX0WyJweWuaN9A@
> >>>> mail.gmail.com
> >>>>
> >>>>>
> >>>>>>  Content-Type: text/plain; charset=UTF-8
> >>>>
> >>>> hello gromacs
> >>>> i an working on protein ligand complex with lipid membrane (popc)
> >>>>
> >>>> grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr
> -maxwarn
> >>>> -1
> >>>>
> >>>> after this fatal error atomtypes CA not found
> >>>> and only md.oonly mdout is formed
> >>>> kindly help
> >>>>
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> --
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> >>>>
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> >>>>
> >>>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >>
> >> --
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> >>
> >
> >
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-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

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